Test PR for PCVCOMM #38

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open

Iximiel wants to merge 124 commits into master from pycvComm

.github/workflows/dockerWF.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -29,3 +29,6 @@ jobs: @@
         - name: Build and run tests
           run: |
             make -C docker ${{ matrix.variant }}
+        - name: PyCV tests
+          run: |
+            make -C docker ${{ matrix.variant }}-pycv

.github/workflows/linuxWF.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -24,6 +24,7 @@ jobs: @@
             - -coverage-mpi-
             - -debug-
             - -debug-mpi-
+            - -pycv-mpi-
     # temporarily commented out
     # see https://github.com/plumed/plumed2/issues/976
     #        - -intel-
@@ Expand Down Expand Up / @@ -148,7 +149,7 @@ jobs: @@
             make nmcheck
             ccache -s -M 100M
         - name: Run tests
-          if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) }}
+          if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) && ! contains( matrix.variant, '-pycv-mpi-' ) }}
           run: |
              (while true; do  # see https://github.com/actions/virtual-environments/issues/1860
                   df -h
@@ Expand Down Expand Up / @@ -181,3 +182,12 @@ jobs: @@
             GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
           run: |
              .ci/push doc
+        - name: Compile and test pycv
+          if: contains( matrix.variant, '-pycv-' )
+          working-directory: ./plugins/pycv/
+          run: |
+                pip install --user pybind11
+                source ../../sourceme.sh
+                ln -s $(realpath ../../regtest/scripts) ./regtest/scripts
+                ./prepareMakeForDevelop.sh
+                make check

docker/Makefile

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,14 +1,20 @@
  
    .PHONY: ubuntu plumed2.tgz clean fedora38 rocky8

    .PHONY: ubuntu plumed2.tgz clean fedora38 fedora38-pycv rocky8 rocky8-pycv 

    ubuntu: plumed2.tgz

    	docker build -t plumed .

    	docker build -t plumed --progress=plain .

    fedora38: plumed2.tgz

    	docker build -t plumed -f fedora38 .

    	docker build -t plumed:fedora38 --progress=plain -f fedora38 .

    fedora38-pycv: plumed2.tgz

    	docker build -t plumed:fedora38-pycv --progress=plain -f fedora38-pycv .

    rocky8: plumed2.tgz

    	docker build -t plumed -f rocky8 .

    	docker build -t plumed:rocky8 --progress=plain -f rocky8 .

    rocky8-pycv: plumed2.tgz

    	docker build -t plumed:rocky8-pycv --progress=plain -f rocky8-pycv .

    plumed2.tgz:

    	cd ../ ; git archive HEAD -o "$(CURDIR)"/plumed2.tgz --prefix plumed2/ ; cd -

docker/fedora38

Original file line number	Diff line number	Diff line change
Expand Up		@@ -43,4 +43,3 @@ RUN . /etc/bashrc \
		&& ./configure --enable-modules=all --enable-boost_serialization \
		&& make -j 4 \
		&& make check

docker/fedora38-pycv

-Original file line number
+Diff line change
@@ -0,0 +1,11 @@
+    FROM plumed:fedora38
+    RUN source /etc/bashrc \
+     && module load mpi \
+     && cd plumed2 \
+     && source ./sourceme.sh \
+     && cd plugins/pycv \
+     && pip3 install pybind11 \
+     && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
+     && ./prepareMakeForDevelop.sh \
+     && make check

docker/rocky8

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,23 +7,41 @@ RUN yum -y update \ @@
      && dnf config-manager --set-enabled powertools \
      && yum -y group install "Development Tools" \
      && yum -y install environment-modules gawk vim wget \
-                       lapack-devel blas-devel zlib-devel gsl-devel fftw-devel openmpi-devel boost-devel \
-                       python3 python3-devel python3-pip \
-     && pip3 install pillow==8.3.2 \
-     && pip3 install numpy==1.19 \
-     && pip3 install "cython<3" numpy pandas mdtraj \
-     && pip3 install MDAnalysis==1.0.0
+     lapack-devel blas-devel zlib-devel gsl-devel fftw-devel openmpi-devel boost-devel \
+     openssl-devel libffi-devel
     RUN useradd -ms /bin/bash plumed
+    #These are needed for installing python
     USER plumed
     WORKDIR /home/plumed
+    #Install python with --embedded
+    #COPY installPythonForDocker.sh /home/plumed
+    RUN PYVERSION="3.9.16" \
+     && curl -LO https://www.python.org/ftp/python/${PYVERSION}/Python-${PYVERSION}.tgz \
+     && tar xzf Python-${PYVERSION}.tgz \
+     && cd Python-${PYVERSION} \
+     && ./configure --enable-shared --prefix=$HOME/.local \
+     && make -j 4 \
+     && make install \
+     && echo "export LD_LIBRARY_PATH=$HOME/.local/lib/${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}" >> "$HOME/.bashrc"
+    RUN . ./.bashrc \
+     && pip3 install --user -U pip \
+     && pip3 install --user pillow==8.3.2 \
+     && pip3 install --user "Cython<3" \
+     && pip3 install --user pandas \
+     && pip3 install --user mdtraj     \
+     && pip3 install --user MDAnalysis==1.0.0
+    #  && pip3 install --user numpy==1.19
     # import plumed code.
     # assumes a file plumed2.tgz is present in the Dockerfile directory
     COPY plumed2.tgz /home/plumed
     # build and test plumed (no install)
-    RUN . /etc/bashrc \
+    RUN . ./.bashrc \
      && module load mpi \
      && export OMPI_MCA_btl_base_warn_component_unused=0 \
      && export OMPI_MCA_btl_base_verbose=0 \
@@ Expand All / @@ -42,4 +60,3 @@ RUN . /etc/bashrc \ @@
      && ./configure --enable-modules=all --enable-boost_serialization \
      && make -j 4 \
      && make check

docker/rocky8-pycv

-Original file line number
+Diff line change
@@ -0,0 +1,11 @@
+    FROM plumed:rocky8
+    RUN source ./.bashrc \
+     && module load mpi \
+     && cd plumed2 \
+     && source ./sourceme.sh \
+     && cd plugins/pycv \
+     && pip3 install --user pybind11  \
+     && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
+     && ./prepareMakeForDevelop.sh \
+     && make check

plugins/pycv/.gitignore

-Original file line number
+Diff line change
@@ -0,0 +1,4 @@
+    Make.inc
+    *.o
+    *.so
+    env

plugins/pycv/ActionWithPython.cpp

-Original file line number
+Diff line change
@@ -0,0 +1,142 @@
+    /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    Copyright (c) 2019 of Toni Giorgino
+    The pycv module is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    The pycv module is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+    You should have received a copy of the GNU Lesser General Public License
+    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+    #include "ActionWithPython.h"
+    #include "core/ActionWithValue.h"
+    #include <pybind11/embed.h> // everything needed for embedding
+    #include <pybind11/numpy.h>
+    #include <iostream>
+    namespace py = pybind11;
+    namespace PLMD {
+    namespace pycv {
+    // We can only have one interpreter globally. This is less than ideal
+    // because CVs can interfere with each other. The whole purpose of
+    // this superclass is to make a singleton. Putting it in the
+    // constructor makes it so that the interpreter is only initialized if
+    // one of the PYCV actions are used.
+    // https://pybind11.readthedocs.io/en/stable/reference.html#_CPPv422initialize_interpreterb
+    unsigned PlumedScopedPythonInterpreter::use_count=0;
+    std::unique_ptr<py::scoped_interpreter> PlumedScopedPythonInterpreter::interpreterGuard =
+      nullptr;
+    std::mutex PlumedScopedPythonInterpreter::interpreterMutex{};
+    PlumedScopedPythonInterpreter::PlumedScopedPythonInterpreter(::PLMD::Log&outlog)
+      :log(outlog) {
+      std::lock_guard<std::mutex> lk(interpreterMutex);
+      if(use_count==0 && Py_IsInitialized()) {
+        //this addresses the "calling pycv within a python interpreter problem"
+        ++use_count;
+      }
+      if(use_count==0) {
+        std::cerr<< "------ initialized Python interpreter\n";
+        log<< "------ initialized Python interpreter\n";
+        interpreterGuard = std::make_unique<py::scoped_interpreter>();
+      } else {
+        std::cerr << "------ Python interpreter already initializated\n";
+        log << "------ Python interpreter already initializated\n";
+      }
+      ++use_count;
+    }
+    PlumedScopedPythonInterpreter::~PlumedScopedPythonInterpreter() {
+      // Finalization is tricky, because it should happen AFTER the
+      // destruction of ALL the python declared variables
+      std::lock_guard<std::mutex> lk(interpreterMutex);
+      --use_count;
+      if(use_count==0) {
+        interpreterGuard.reset(nullptr);
+        std::cerr << "------ Python interpreter finalized\n";
+        log << "------ Python interpreter finalized\n";
+      }
+    }
+    ActionWithPython::ActionWithPython (const ActionOptions&ao)
+      :Action(ao),guard(log) {}
+    void ActionWithPython::pyParseFlag(const char* key, const ::pybind11::dict &initDict, bool& returnValue) {
+      parseFlag(key, returnValue);
+      if(initDict.contains(key)) {
+        bool defaultRet;
+        keywords.getLogicalDefault(key,defaultRet);
+        if (returnValue!=defaultRet) {
+          error(std::string("you specified the same keyword ").append(key)+ " both in python and in the settings file");
+        }
+        returnValue = initDict[key].cast<bool>();
+      }
+    }
+    /******************************************************************************/
+    //Value/components init
+    void initializeValue(::PLMD::ActionWithValue& action,pybind11::dict &settingsDict) {
+      action.log << "  will have a single component";
+      bool withDerivatives=false;
+      if(settingsDict.contains("derivative")) {
+        withDerivatives=settingsDict["derivative"].cast<bool>();
+      }
+      if(withDerivatives) {
+        action.addValueWithDerivatives();
+        action.log << " WITH derivatives\n";
+      } else {
+        action.addValue();
+        action.log << " WITHOUT derivatives\n";
+      }
+    }
+    void initializeComponent(::PLMD::ActionWithValue& action,const std::string&name,py::dict &settingsDict) {
+      bool withDerivatives=false;
+      if(settingsDict.contains("derivative")) {
+        withDerivatives=settingsDict["derivative"].cast<bool>();
+      }
+      if(withDerivatives) {
+        action.addComponentWithDerivatives(name);
+        action.log << " WITH derivatives\n";
+      } else {
+        action.addComponent(name);
+        action.log << " WITHOUT derivatives\n";
+      }
+    }
+    void valueSettings(py::dict &settings, Value* valPtr) {
+      if(settings.contains("period")) {
+        if (settings["period"].is_none()) {
+          valPtr->setNotPeriodic();
+        } else {
+          py::tuple t = settings["period"];
+          if(t.size()!=2) {
+            plumed_merror("period must have exactly 2 components");
+          }
+          //the ballad py::str(t[0]).cast<std::string>() is to not care about the type of input of the user
+          std::string min=py::str(t[0]).cast<std::string>();
+          std::string max=py::str(t[1]).cast<std::string>();
+          valPtr->setDomain(min, max);
+        }
+      }
+    }
+    } // namespace pycv
+    } // namespace PLMD

plugins/pycv/ActionWithPython.h

-Original file line number
+Diff line change
@@ -0,0 +1,81 @@
+    /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    Copyright (c) 2019 of Toni Giorgino
+    The pycv module is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    The pycv module is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+    You should have received a copy of the GNU Lesser General Public License
+    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+    #ifndef __PLUMED_pycv_ActionWithPython_h //{
+    #define __PLUMED_pycv_ActionWithPython_h
+    #include <mutex>
+    #include <string>
+    #include "core/Action.h"
+    #include <pybind11/embed.h> // everything needed for embedding
+    namespace PLMD {
+    class Value;
+    namespace pycv {
+    using pycvComm_t = double;
+    static constexpr auto PYTHONCV_CITATION = "Giorgino, (2019). PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python. Journal of Open Source Software, 4(42), 1773. doi:10.21105/joss.01773";
+    static constexpr auto BIASING_DISABLED = "PYCV: Gradient was expected as a second return value but is missing. Biasing won't work\n";
+    static constexpr std::string_view PYCV_COMPONENTPREFIX="py";
+    ///This class act both as a guard for the interpreter and a a case container for the python module and functions
+    class PlumedScopedPythonInterpreter final {
+    public:
+      PlumedScopedPythonInterpreter(::PLMD::Log&);
+      ~PlumedScopedPythonInterpreter();
+    private:
+      ::PLMD::Log& log;
+      static unsigned use_count;
+      static std::unique_ptr<::pybind11::scoped_interpreter> interpreterGuard;
+      static std::mutex interpreterMutex;
+    };
+    class ActionWithPython: public virtual ::PLMD::Action {
+      //the guard MUST be set up before the python objects
+      // (so that it can be destroyed after them)
+      PlumedScopedPythonInterpreter guard;
+    public:
+      explicit ActionWithPython (const ActionOptions&);
+      ///redefinition of parse to avoid confict between plumed.dat and python options
+      template<typename T>
+      void pyParse(const char* key, const ::pybind11::dict &initDict, T& returnValue);
+    ///redefinition of parseFlag to avoid confict between plumed.dat and python options
+      void pyParseFlag(const char* key, const ::pybind11::dict &initDict, bool& returnValue);
+    };
+    template<typename T>
+    void ActionWithPython::pyParse(
+      const char* key, const ::pybind11::dict &initDict, T& returnValue) {
+      T initVal(returnValue);
+      parse(key,returnValue);
+      //this is not robust, but with no access to Action::line we cannot use Tools::findKeyword
+      if(initDict.contains(key)) {
+        if (returnValue != initVal) {
+          error(std::string("you specified the same keyword ").append(key)+ " both in python and in the settings file");
+        }
+        returnValue = initDict[key].cast<T>();
+      }
+    }
+    void initializeValue(::PLMD::ActionWithValue&, pybind11::dict &);
+    void initializeComponent(::PLMD::ActionWithValue&,const std::string&,pybind11::dict &);
+    void valueSettings( pybind11::dict &r, Value* valPtr);
+    } // namespace pycv
+    } // namespace PLMD
+    #endif //__PLUMED_pycv_ActionWithPython_h //}

plugins/pycv/COPYRIGHT

-Original file line number
+Diff line change
@@ -0,0 +1,14 @@
+    Copyright (c) 2019 of Toni Giorgino
+    The pycv module is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    The pycv module is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+    You should have received a copy of the GNU Lesser General Public License
+    along with plumed.  If not, see <http://www.gnu.org/licenses/>.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Test PR for PCVCOMM #38

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Uh oh!

Test PR for PCVCOMM #38

Are you sure you want to change the base?

Uh oh!

Test PR for PCVCOMM #38

Uh oh!

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Uh oh!